The Brit, who is a judge on the show and an executive producer on American Idol, hit out at contestants Misha Belfer and Mitchel Kibel after they performed a same-sex samba routine.
In the show's season premiere on Thursday, Lythgoe told the pair, "I think you probably alienate a lot of our audience. I mean, we've always had the guys dance together on the show, but they've never really done it in each other's arms before.
"Do you know what? I'd like to see you both dancing with a girl."
After the show, Lythgoe also backed-up his comments on the panel by taking to his online blog, writing: "The same-sex ballroom guys did remind me of Blades of Glory. However, I'm not a fan of Brokeback ballroom."
But his comments have been blasted by officials at gay-rights group GLAAD, who are demanding an apology from the TV titan.
GLAAD president Neil G. Giuliano says, "It's unacceptable for this kind of blatant homophobia to occur. Fox Entertainment and Nigel Lythgoe owe Misha, Mitchel and the whole LGBT community an apology."
(c) 2009 WORLD ENTERTAINMENT NEWS NETWORK LTD. All global rights reserved. No unauthorized copying or re-distributing permitted.